As marine aquaculture expands around the world, there is increased concern for impacts to protected species. Documented cases of marine mammal, sea turtle, seabird, and shark interactions with aquaculture installations do exist but are challenging to find. This extensive review summarises the state of knowledge of protected species interactions with marine fish and shellfish aquaculture installations. Although seaweed aquaculture was beyond the scope of this review, some of the findings for shellfish and finfish aquaculture may be relevant. The potential impacts of farms including habitat exclusion, entanglement, entrapment, collisions, and behavioural modifications are the primary risks posed to protected species by marine aquaculture facilities and operations. In addition, indirect effects from habitat impacts of farm operations may be of concern in some areas as well as the cumulative impacts of multiple small or large farms in the same general vicinity. Decades of farm innovations and best management practices have been driven by industry, natural resource managers, conservation organisations, and international conservation agreements. This review is useful for informing industry planning and permitting to develop aquaculture in the open ocean. This work will help advance the science of conservation by synthesising the state of knowledge and provide managers and industry with more insight to protect the most vulnerable species.